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        <H2>OMSSA Viewer</H2>
        <p align="justify">
            OMSSA Viewer is a simple, lightweight viewer of
            <a href="http://pubchem.ncbi.nlm.nih.gov/omssa/">OMSSA</a> MS/MS
            result files (OMX files). The input is the OMX file itself and
            (if available) two files containing details about the amino acid
            modification that was used by OMSSA in the identification process:
            mods.xml and usermods.xml. Both of these are located in the OMSSA
            installation directory. If you don't have these files available
            you will still be able to use OMSSA Viewer, but no modifications
            will be shown.
            <br><br>
            After selecting the files, OMSSA Viewer uses the omssa-parser
            to parse the OMX file into an object model that is then used to
            extract the information to present to the user. OMSSA Viewer
            has three separate sections: (i) the Spectrum Files, (ii) the
            Selected Spectrum, and (iii) the Identifications. The Spectrum
            Files section contains the basic details about each spectrum file:
            the filename, the precursor m/z and charge, and if it's identified
            or not. Selecting a row in this table, automatically updates the
            two other panels, by displaying all the identification for the
            given spectrum and by displaying the spectrum itself. Clicking on
            a column header will automatically sort the table on the values
            in the given column.
            <br><br>
            For the spectra identified by OMSSA, the ion coverage is shown.
            Both on the spectra and in the modified sequence column in the
            identification table. By selecting two peaks in the spectrum
            panel the distance between the peaks is shown. If this
            distance has a mass equal to an amino acid the given amino acid
            is also displayed.
            <br><br>
            The information in each of the three tables can be exported to
            tab delimited text files. This is done via the
            Export menu. It is also possible to export the spectra as
            individual dta files.
            <br><br>
            If you want to submit your OMSSA data to the online
            <a href="http://www.ebi.ac.uk/pride/">PRIDE</a>
            repository check out the
            <a href="http://pride-converter.googlecode.com/">PRIDE Converter</a>.
            <br><br>
            For a more advanced viewer of OMSSA search results we recommend <a href="http://peptide-shaker.googlecode.com">PeptideShaker</a>.
            <br><br>
        </p>

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